What is literature-survey?

A workflow for building a checked and reusable collection of research-paper references. It includes BibTeX records, published-paper PDFs, extracted text, notes for each paper, and a log of verification work.

Starting or maintaining a literature review, verifying references, adding papers to a BibTeX file, and writing structured notes about each paper.

It helps prevent incorrect, missing, or unverified references from entering a paper's bibliography.

literature-survey — Skill for Claude Code and Codex by a-attia

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add a-attia/scicomp-research-skills --skill literature-survey

Clone the repo

git clone --depth 1 https://github.com/a-attia/scicomp-research-skills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/a-attia/scicomp-research-skills/literature-survey/github.svg)](https://agentmods.dev/skills/a-attia/scicomp-research-skills/literature-survey)

Your own site

<a href="https://agentmods.dev/skills/a-attia/scicomp-research-skills/literature-survey"><img src="https://agentmods.dev/badge/skills/a-attia/scicomp-research-skills/literature-survey/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/a-attia/scicomp-research-skills/literature-survey"><img src="https://agentmods.dev/badge/skills/a-attia/scicomp-research-skills/literature-survey.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 128 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 3,095 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

NVIDIA SkillSpector warn 7 Sept 2026

SkillSpector: 4 findings, up to medium

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

medium Rogue Agent · line 38
Skill establishes unauthorized persistence across sessions via cron jobs, startup scripts, or state files. Session persistence allows an attacker to maintain access beyond the current interaction.

Fix: Remove any persistence mechanisms (cron jobs, startup scripts, state files). Skills should not maintain state across sessions without explicit user consent.
medium Agent Snooping · line 205
Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.

Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
medium Agent Snooping · line 235
Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.

Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
medium Agent Snooping · line 240
Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.

Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.

How audits are shown

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00128	$0.03095
Opus 5.5	$0.00051	$0.01238
Sonnet 5.5	$0.00026	$0.00619
Haiku 4.5	$0.00013	$0.00310

Measured 22d ago against content hash 2094f7819f05, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

literature-survey scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 22d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/literature-survey/SKILL.md · 293 lines

How it starts

The opening of the file, as written. The whole thing — 293 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Literature Survey

When to load this skill

Load this skill when the user is:

looking for related work, prior art, or papers on a topic (Step 0)
starting a new research paper that needs a literature review
adding new references to an existing paper
migrating an unverified BibTeX file to a verified one
doing a deep-read pass on a set of references and producing per-paper notes
needing a reproducible record of which references have been verified vs which are still placeholders

Overview

A research paper's bibliography drives credibility. Stale, mis-attributed, or unverified entries embarrass the author at submission time. This skill defines a workflow of five steps plus an optional Step 0 (finding candidates) for building a verified literature corpus and a deliverables structure that future-you (or a collaborator) can audit and extend.

The steps:

(When candidates are not yet in hand) Find them: see "Step 0" below.
Add a verified BibTeX entry to references/bibliography.bib.
Drop the published-manuscript PDF into references/pdf/<citekey>.pdf.
Generate a text extraction for AI consumption.
Write a survey note notes/survey_<citekey>.md.
Append a row to references/_collection_log.md.

Each step is described in detail below, plus the directory layout, the survey-note template, and the collection-log template.

Directory layout

<paper-repo>/
  references/
    bibliography.bib          -- BibTeX (tracked); every entry verified
    _collection_log.md        -- per-paper verification status + corrections + notes
    pdf/                      -- published-manuscript PDFs (gitignored)
      <citekey>.pdf
      <citekey>-supp.pdf      -- supplementary material where applicable
      .txt/                   -- pdftotext -layout extractions (gitignored)
        <citekey>.txt
  notes/
    survey_<citekey>.md       -- per-paper survey note (~30-50 lines)
    README.md                 -- index of survey notes (by section, by affinity)

Read the full file on GitHub · 293 lines

Files

What ships with it

4 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

22d ago Changed · +30 lines · +35 tokens per session 2094f7819f05
2mo ago First seen · 263 lines · 93 tokens per session scan A 967156abae6a

Subscribe to this mod's changes

literature-survey is a skill published in the GitHub repository a-attia/scicomp-research-skills (13 stars, last pushed 23d ago), licensed MIT. It adds 128 tokens to every session and 3,095 once invoked, about $0.0005 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Research

literature-survey next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
literature-surveya-attia/scicomp-research-skills	Skill	13	23d ago	MIT	A	128	Claude Code, Codex
imagegenopenai/codex	Skill	133k	yesterday	Apache-2.0	A	113	Codex
playwright-climicrosoft/playwright	Skill	99k	yesterday	Apache-2.0	A	19	Claude Code
local-ai-agentsmicrosoft/ai-agents-for-beginners	Skill	79k	4d ago	MIT	A	200	Claude Code, Codex
systematic-debuggingobra/superpowers	Skill	313k	3d ago	MIT	A	21	Claude Code
next-cache-components-adoptionvercel/next.js	Skill	143k	yesterday	MIT	A	95	Claude Code
next-partial-prefetching-adoptionvercel/next.js	Skill	143k	yesterday	MIT	A	103	Claude Code